Although the neural circuits underlying fear learning are among the best characterized of any mammalian neural circuit, the specific circuit mechanisms by which fear memories are encoded in the brain remain poorly defined. Until this gap in knowledge is closed, it will likely remain difficult to effectively and specifically treat axiety and post-traumatic stress disorders. A long-term strategy to approach this problem is to combine electrophysiological and optogenetic tools with molecular tools that allow specific populations of neurons to be labeled and manipulated. However, molecular access to specific neural populations within the fear circuit remains limited. The specific objective here is to identfy molecular markers for specific subsets of neurons within the basolateral complex of the amygdala, a brain region required for fear learning. The proposed work will pilot a new strategy for identifying molecular markers of functionally relevant neural populations, based on manual sorting and RNA sequencing of small numbers of labeled neurons. Neurons will be labeled based on their activity history and their projection targets. The markers identified in the proposed work will be immediately useful for genetic labeling and manipulation of specific populations of neurons within the fear learning circuit. The overall hypothesis is that the neurons engaged during fear learning represent specific subpopulations of principal neurons defined by their anatomical and functional circuit connectivity. This hypothesis will be tested by two specifi aims: (1) defining the complement of genes expressed by each of several classes of basolateral complex projection neurons; and (2) defining the complement of genes expressed in the specific subset of amygdala neurons transcriptionally activated during fear learning. The contribution here is significant because it will correct a long-standing barrier to understanding fear learning by identifying molecular markers for specific subclasses of principal neurons. It is innovative in its combined application of low-input RNA-Seq technologies, retrograde labeling of neural projections, and transcriptional reporters of neural activity. These tools collectively represent a promising new strategy to comprehensively identify molecular markers for functionally important neural circuits.